Starting phenix.real_space_refine
on Sun Nov 17 00:46:48 2024 by dcliebschner
===============================================================================

Processing files:
-------------------------------------------------------------------------------

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s4v_24835/11_2024/7s4v_24835.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s4v_24835/11_2024/7s4v_24835.map

Processing PHIL parameters:
-------------------------------------------------------------------------------

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.28
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s4v_24835/11_2024/7s4v_24835.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s4v_24835/11_2024/7s4v_24835.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s4v_24835/11_2024/7s4v_24835.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s4v_24835/11_2024/7s4v_24835.cif"
  }
  resolution = 3.28
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.015
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P     141      5.49       5
     S      18      5.16       5
     C    7249      2.51       5
     N    2149      2.21       5
     O    2658      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 15 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib"
  Total number of atoms: 12215
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 9167
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1122, 9167
          Classifications: {'peptide': 1122}
          Link IDs: {'PTRANS': 30, 'TRANS': 1091}
          Chain breaks: 5
    Chain: "B"
      Number of atoms: 2100
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 2100
          Classifications: {'RNA': 98}
          Modifications used: {'5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 6, 'rna3p_pur': 52, 'rna3p_pyr': 33}
          Link IDs: {'rna2p': 13, 'rna3p': 84}
    Chain: "C"
      Number of atoms: 665
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 33, 665
          Classifications: {'DNA': 33}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 32}
    Chain: "D"
      Number of atoms: 283
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 14, 283
          Inner-chain residues flagged as termini: ['pdbres=" DC D  30 "']
          Classifications: {'DNA': 14}
          Modifications used: {'5*END': 2}
          Link IDs: {'rna3p': 13}
  Time building chain proxies: 7.99, per 1000 atoms: 0.65
  Number of scatterers: 12215
  At special positions: 0
  Unit cell: (88, 143, 129.8, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      18     16.00
     P     141     15.00
     O    2658      8.00
     N    2149      7.00
     C    7249      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.02
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2140

  Finding SS restraints...
    Secondary structure from input PDB file:
      59 helices and 7 sheets defined
      54.2% alpha, 8.2% beta
      22 base pairs and 73 stacking pairs defined.
    Time for finding SS restraints: 4.23
  Creating SS restraints...
    Processing helix  chain 'A' and resid 59 through 94
      removed outlier: 3.673A  pdb=" N   ARG A  63 " --> pdb=" O   ALA A  59 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   ARG A  74 " --> pdb=" O   ARG A  70 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   ARG A  75 " --> pdb=" O   ARG A  71 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   LYS A  76 " --> pdb=" O   TYR A  72 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   ASN A  77 " --> pdb=" O   THR A  73 " (cutoff:3.500A)
      removed outlier: 4.069A  pdb=" N   LEU A  82 " --> pdb=" O   ARG A  78 " (cutoff:3.500A)
      removed outlier: 5.504A  pdb=" N   ASN A  88 " --> pdb=" O   GLU A  84 " (cutoff:3.500A)
      removed outlier: 5.546A  pdb=" N   GLU A  89 " --> pdb=" O   ILE A  85 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   LYS A  92 " --> pdb=" O   ASN A  88 " (cutoff:3.500A)
      removed outlier: 3.933A  pdb=" N   VAL A  93 " --> pdb=" O   GLU A  89 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   ASP A  94 " --> pdb=" O   MET A  90 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 96 through 104
    Processing helix  chain 'A' and resid 122 through 132
    Processing helix  chain 'A' and resid 134 through 145
      removed outlier: 4.059A  pdb=" N   LEU A 138 " --> pdb=" O   THR A 134 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 150 through 164
    Processing helix  chain 'A' and resid 175 through 180
    Processing helix  chain 'A' and resid 181 through 183
      No H-bonds generated for 'chain 'A' and resid 181 through 183'
    Processing helix  chain 'A' and resid 184 through 196
    Processing helix  chain 'A' and resid 207 through 214
    Processing helix  chain 'A' and resid 217 through 229
      removed outlier: 3.928A  pdb=" N   GLU A 223 " --> pdb=" O   SER A 219 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 238
      removed outlier: 3.571A  pdb=" N   PHE A 238 " --> pdb=" O   LYS A 234 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 240 through 246
    Processing helix  chain 'A' and resid 270 through 275
    Processing helix  chain 'A' and resid 275 through 280
      removed outlier: 4.185A  pdb=" N   ALA A 280 " --> pdb=" O   ASP A 276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 289 through 304
      removed outlier: 3.949A  pdb=" N   LYS A 294 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   ASN A 295 " --> pdb=" O   LEU A 291 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 315 through 343
      removed outlier: 3.548A  pdb=" N   ALA A 319 " --> pdb=" O   ALA A 315 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 346 through 352
      removed outlier: 3.627A  pdb=" N   PHE A 352 " --> pdb=" O   LYS A 348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 359 through 364
    Processing helix  chain 'A' and resid 368 through 382
      Proline residue:  A 378  - end of helix
      removed outlier: 3.919A  pdb=" N   LYS A 382 " --> pdb=" O   PRO A 378 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 386 through 394
      removed outlier: 3.500A  pdb=" N   ASN A 394 " --> pdb=" O   LEU A 390 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 404 through 410
      removed outlier: 3.645A  pdb=" N   ASN A 407 " --> pdb=" O   THR A 404 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   SER A 409 " --> pdb=" O   ASP A 406 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   ILE A 410 " --> pdb=" O   ASN A 407 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 411 through 427
      removed outlier: 4.164A  pdb=" N   HIS A 415 " --> pdb=" O   PRO A 411 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   GLY A 417 " --> pdb=" O   GLN A 413 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   GLN A 426 " --> pdb=" O   ILE A 422 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 430 through 436
      removed outlier: 3.960A  pdb=" N   LYS A 434 " --> pdb=" O   TYR A 430 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 436 through 445
      removed outlier: 3.649A  pdb=" N   ILE A 440 " --> pdb=" O   ASN A 436 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 477 through 481
      removed outlier: 3.552A  pdb=" N   GLU A 480 " --> pdb=" O   ASN A 477 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 484 through 494
      removed outlier: 3.862A  pdb=" N   ILE A 492 " --> pdb=" O   ALA A 488 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 512 through 525
    Processing helix  chain 'A' and resid 541 through 553
      removed outlier: 3.906A  pdb=" N   ASP A 550 " --> pdb=" O   LYS A 546 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 560 through 567
      removed outlier: 3.554A  pdb=" N   LEU A 564 " --> pdb=" O   THR A 560 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 568 through 572
      removed outlier: 4.053A  pdb=" N   LYS A 571 " --> pdb=" O   TYR A 568 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 573 through 576
      removed outlier: 4.299A  pdb=" N   ASP A 576 " --> pdb=" O   GLU A 573 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 573 through 576'
    Processing helix  chain 'A' and resid 591 through 602
    Processing helix  chain 'A' and resid 604 through 609
    Processing helix  chain 'A' and resid 612 through 626
      removed outlier: 3.989A  pdb=" N   LEU A 621 " --> pdb=" O   GLU A 617 " (cutoff:3.500A)
      removed outlier: 3.879A  pdb=" N   LEU A 623 " --> pdb=" O   ILE A 619 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 628 through 637
    Processing helix  chain 'A' and resid 638 through 643
      removed outlier: 4.928A  pdb=" N   HIS A 641 " --> pdb=" O   THR A 638 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 644 through 652
    Processing helix  chain 'A' and resid 663 through 668
      removed outlier: 3.814A  pdb=" N   ILE A 667 " --> pdb=" O   SER A 663 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 678 through 686
    Processing helix  chain 'A' and resid 692 through 698
    Processing helix  chain 'A' and resid 705 through 712
      removed outlier: 3.547A  pdb=" N   GLN A 709 " --> pdb=" O   LYS A 705 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 720 through 725
    Processing helix  chain 'A' and resid 730 through 751
      removed outlier: 3.579A  pdb=" N   LYS A 734 " --> pdb=" O   SER A 730 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   LYS A 742 " --> pdb=" O   LEU A 738 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   MET A 751 " --> pdb=" O   LEU A 747 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 926 through 940
    Processing helix  chain 'A' and resid 960 through 970
      removed outlier: 3.603A  pdb=" N   SER A 964 " --> pdb=" O   SER A 960 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   PHE A 970 " --> pdb=" O   PHE A 966 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 981 through 998
    Processing helix  chain 'A' and resid 1079 through 1088
      removed outlier: 4.028A  pdb=" N   VAL A1083 " --> pdb=" O   ASP A1079 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1127 through 1132
    Processing helix  chain 'A' and resid 1170 through 1177
    Processing helix  chain 'A' and resid 1177 through 1184
    Processing helix  chain 'A' and resid 1229 through 1240
      removed outlier: 3.627A  pdb=" N   SER A1240 " --> pdb=" O   LEU A1236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1248 through 1251
    Processing helix  chain 'A' and resid 1252 through 1262
      removed outlier: 3.533A  pdb=" N   GLN A1256 " --> pdb=" O   ASN A1252 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1264 through 1280
      removed outlier: 4.380A  pdb=" N   GLU A1268 " --> pdb=" O   HIS A1264 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1283 through 1296
    Processing helix  chain 'A' and resid 1301 through 1310
    Processing helix  chain 'A' and resid 1311 through 1316
      removed outlier: 3.766A  pdb=" N   THR A1314 " --> pdb=" O   HIS A1311 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1339 through 1343
      removed outlier: 3.940A  pdb=" N   VAL A1342 " --> pdb=" O   THR A1339 " (cutoff:3.500A)
      removed outlier: 3.896A  pdb=" N   LEU A1343 " --> pdb=" O   LYS A1340 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1339 through 1343'
    Processing helix  chain 'A' and resid 1363 through 1365
      No H-bonds generated for 'chain 'A' and resid 1363 through 1365'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 956 through 957
      removed outlier: 6.144A  pdb=" N   ILE A 759 " --> pdb=" O   ILE A 956 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   VAL A1095 " --> pdb=" O   ALA A  50 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 29 through 32
    Processing sheet with id=AA3, first strand: chain 'A' and resid 34 through 35
      removed outlier: 6.114A  pdb=" N   LEU A  35 " --> pdb=" O   ARG A1359 " (cutoff:3.500A)
      removed outlier: 7.725A  pdb=" N   ASP A1361 " --> pdb=" O   LEU A  35 " (cutoff:3.500A)
      removed outlier: 4.590A  pdb=" N   LEU A1203 " --> pdb=" O   ILE A1348 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   ARG A1210 " --> pdb=" O   LEU A1206 " (cutoff:3.500A)
      removed outlier: 6.433A  pdb=" N   GLU A1219 " --> pdb=" O   ALA A1215 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 530 through 531
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1156 through 1162
      removed outlier: 3.648A  pdb=" N   LYS A1156 " --> pdb=" O   LYS A1151 " (cutoff:3.500A)
      removed outlier: 7.210A  pdb=" N   ILE A1166 " --> pdb=" O   ALA A1140 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1156 through 1162
      removed outlier: 3.648A  pdb=" N   LYS A1156 " --> pdb=" O   LYS A1151 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   ILE A1196 " --> pdb=" O   LEU A1144 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 1324 through 1325
      removed outlier: 3.592A  pdb=" N   PHE A1324 " --> pdb=" O   ILE A1331 " (cutoff:3.500A)

    380 hydrogen bonds defined for protein.
    1101 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      57 hydrogen bonds
      110 hydrogen bond angles
      0 basepair planarities
      22 basepair parallelities
      73 stacking parallelities
  Total time for adding SS restraints: 6.00

  Time building geometry restraints manager: 3.52 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.21 -     1.33: 3053
        1.33 -     1.45: 3123
        1.45 -     1.58: 6250
        1.58 -     1.70: 282
        1.70 -     1.82: 34
  Bond restraints: 12742
  Sorted by residual:
  bond pdb=" CB  PRO A 503 "
       pdb=" CG  PRO A 503 "
    ideal  model  delta    sigma   weight residual
    1.492  1.563 -0.071 5.00e-02 4.00e+02 1.99e+00
  bond pdb=" CA  MET A 751 "
       pdb=" C   MET A 751 "
    ideal  model  delta    sigma   weight residual
    1.525  1.541 -0.016 1.38e-02 5.25e+03 1.31e+00
  bond pdb=" C3'  DG C  11 "
       pdb=" O3'  DG C  11 "
    ideal  model  delta    sigma   weight residual
    1.422  1.452 -0.030 3.00e-02 1.11e+03 1.00e+00
  bond pdb=" CD  GLU A1260 "
       pdb=" OE1 GLU A1260 "
    ideal  model  delta    sigma   weight residual
    1.249  1.230  0.019 1.90e-02 2.77e+03 9.75e-01
  bond pdb=" C3'  DC D   2 "
       pdb=" O3'  DC D   2 "
    ideal  model  delta    sigma   weight residual
    1.422  1.451 -0.029 3.00e-02 1.11e+03 9.53e-01
  ... (remaining 12737 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.73: 17517
        1.73 -     3.45: 267
        3.45 -     5.18: 36
        5.18 -     6.90: 6
        6.90 -     8.63: 2
  Bond angle restraints: 17828
  Sorted by residual:
  angle pdb=" N   GLU A1260 "
        pdb=" CA  GLU A1260 "
        pdb=" CB  GLU A1260 "
      ideal   model   delta    sigma   weight residual
     110.16  115.21   -5.05 1.48e+00 4.57e-01 1.17e+01
  angle pdb=" N   VAL A 481 "
        pdb=" CA  VAL A 481 "
        pdb=" C   VAL A 481 "
      ideal   model   delta    sigma   weight residual
     111.62  109.03    2.59 7.90e-01 1.60e+00 1.08e+01
  angle pdb=" CA  MET A 751 "
        pdb=" CB  MET A 751 "
        pdb=" CG  MET A 751 "
      ideal   model   delta    sigma   weight residual
     114.10  119.97   -5.87 2.00e+00 2.50e-01 8.61e+00
  angle pdb=" C   MET A 534 "
        pdb=" CA  MET A 534 "
        pdb=" CB  MET A 534 "
      ideal   model   delta    sigma   weight residual
     110.79  115.49   -4.70 1.63e+00 3.76e-01 8.32e+00
  angle pdb=" CB  MET A 694 "
        pdb=" CG  MET A 694 "
        pdb=" SD  MET A 694 "
      ideal   model   delta    sigma   weight residual
     112.70  121.33   -8.63 3.00e+00 1.11e-01 8.27e+00
  ... (remaining 17823 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.01: 7237
       35.01 -    70.03: 436
       70.03 -   105.04: 29
      105.04 -   140.06: 1
      140.06 -   175.07: 7
  Dihedral angle restraints: 7710
    sinusoidal: 4411
      harmonic: 3299
  Sorted by residual:
  dihedral pdb=" O4'   C B  70 "
           pdb=" C1'   C B  70 "
           pdb=" N1    C B  70 "
           pdb=" C2    C B  70 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   54.05  145.95     1      1.50e+01 4.44e-03 7.80e+01
  dihedral pdb=" CA  LEU A 258 "
           pdb=" C   LEU A 258 "
           pdb=" N   ALA A 259 "
           pdb=" CA  ALA A 259 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.00   28.00     0      5.00e+00 4.00e-02 3.14e+01
  dihedral pdb=" C4'  DC D   2 "
           pdb=" C3'  DC D   2 "
           pdb=" O3'  DC D   2 "
           pdb=" P    DT D   3 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -140.00   35.07 -175.07     1      3.50e+01 8.16e-04 1.56e+01
  ... (remaining 7707 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.043: 1649
       0.043 -    0.086: 343
       0.086 -    0.129: 57
       0.129 -    0.173: 10
       0.173 -    0.216: 2
  Chirality restraints: 2061
  Sorted by residual:
  chirality pdb=" CB  VAL A1259 "
            pdb=" CA  VAL A1259 "
            pdb=" CG1 VAL A1259 "
            pdb=" CG2 VAL A1259 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.41   -0.22 2.00e-01 2.50e+01 1.16e+00
  chirality pdb=" CA  GLU A1260 "
            pdb=" N   GLU A1260 "
            pdb=" C   GLU A1260 "
            pdb=" CB  GLU A1260 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.47e-01
  chirality pdb=" C3'   A B  38 "
            pdb=" C4'   A B  38 "
            pdb=" O3'   A B  38 "
            pdb=" C2'   A B  38 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.31   -0.17 2.00e-01 2.50e+01 7.18e-01
  ... (remaining 2058 not shown)

  Planarity restraints: 1745
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 343 "   -0.044 5.00e-02 4.00e+02   6.70e-02 7.19e+00
        pdb=" N   PRO A 344 "    0.116 5.00e-02 4.00e+02
        pdb=" CA  PRO A 344 "   -0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO A 344 "   -0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A B  69 "    0.031 2.00e-02 2.50e+03   1.43e-02 5.65e+00
        pdb=" N9    A B  69 "   -0.035 2.00e-02 2.50e+03
        pdb=" C8    A B  69 "   -0.002 2.00e-02 2.50e+03
        pdb=" N7    A B  69 "    0.001 2.00e-02 2.50e+03
        pdb=" C5    A B  69 "   -0.000 2.00e-02 2.50e+03
        pdb=" C6    A B  69 "    0.004 2.00e-02 2.50e+03
        pdb=" N6    A B  69 "    0.008 2.00e-02 2.50e+03
        pdb=" N1    A B  69 "    0.002 2.00e-02 2.50e+03
        pdb=" C2    A B  69 "   -0.003 2.00e-02 2.50e+03
        pdb=" N3    A B  69 "   -0.005 2.00e-02 2.50e+03
        pdb=" C4    A B  69 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 502 "   -0.030 5.00e-02 4.00e+02   4.51e-02 3.26e+00
        pdb=" N   PRO A 503 "    0.078 5.00e-02 4.00e+02
        pdb=" CA  PRO A 503 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO A 503 "   -0.025 5.00e-02 4.00e+02
  ... (remaining 1742 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 1082
        2.74 -     3.28: 11247
        3.28 -     3.82: 19240
        3.82 -     4.36: 23326
        4.36 -     4.90: 37704
  Nonbonded interactions: 92599
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 515 "
            pdb=" OP1   C B   5 "
     model   vdw
     2.202 3.040
  nonbonded pdb=" OH  TYR A   5 "
            pdb=" O   HIS A 754 "
     model   vdw
     2.253 3.040
  nonbonded pdb=" N2    G B  73 "
            pdb=" OP2   A B  76 "
     model   vdw
     2.271 3.120
  nonbonded pdb=" OG  SER A 541 "
            pdb=" OE2 GLU A 543 "
     model   vdw
     2.291 3.040
  nonbonded pdb=" O   GLY A 533 "
            pdb=" NH1 ARG A 535 "
     model   vdw
     2.309 3.120
  ... (remaining 92594 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.330
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.430
  Check model and map are aligned:         0.070
  Set scattering table:                    0.120
  Process input model:                     33.830
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.590
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   39.550
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7782
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.071  12742  Z= 0.163
  Angle     :  0.537   8.627  17828  Z= 0.290
  Chirality :  0.037   0.216   2061
  Planarity :  0.004   0.067   1745
  Dihedral  : 19.694 175.071   5570
  Min Nonbonded Distance : 2.202

Molprobity Statistics.
  All-atom Clashscore : 4.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.95 %
    Favored  : 95.05 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.40 %
    Favored  : 99.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.46 (0.24), residues: 1110
  helix: -0.28 (0.23), residues: 518
  sheet: -0.79 (0.55), residues: 101
  loop : -1.71 (0.26), residues: 491

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 476 
 HIS   0.004   0.001   HIS A1262 
 PHE   0.010   0.001   PHE A  97 
 TYR   0.013   0.001   TYR A 325 
 ARG   0.007   0.000   ARG A 951 

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 1.235 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  540 LEU cc_start: 0.6211 (tp) cc_final: 0.5895 (mp)
  outliers start: 0
  outliers final: 0
  residues processed: 81
  average time/residue: 0.3397
  time to fit residues: 38.4019
Evaluate side-chains
  43 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 43
  time to evaluate  : 1.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 105 optimal weight:    3.9990
   chunk 94 optimal weight:    2.9990
   chunk 52 optimal weight:    2.9990
   chunk 32 optimal weight:    2.9990
   chunk 63 optimal weight:    8.9990
   chunk 50 optimal weight:    0.7980
   chunk 97 optimal weight:    0.9990
   chunk 37 optimal weight:    0.0970
   chunk 59 optimal weight:    2.9990
   chunk 72 optimal weight:    2.9990
   chunk 113 optimal weight:    3.9990
   overall best weight:    1.5784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 342 GLN
A 721 HIS
A1256 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7961
moved from start:          0.2155

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042  12742  Z= 0.331
  Angle     :  0.623   9.056  17828  Z= 0.331
  Chirality :  0.040   0.204   2061
  Planarity :  0.004   0.041   1745
  Dihedral  : 20.780 176.262   3192
  Min Nonbonded Distance : 2.242

Molprobity Statistics.
  All-atom Clashscore : 3.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.68 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  0.40 %
    Allowed  :  8.65 %
    Favored  : 90.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.16 (0.24), residues: 1110
  helix:  0.07 (0.22), residues: 535
  sheet: -0.97 (0.52), residues: 107
  loop : -1.66 (0.26), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 476 
 HIS   0.009   0.002   HIS A 167 
 PHE   0.020   0.002   PHE A  97 
 TYR   0.019   0.002   TYR A 325 
 ARG   0.006   0.001   ARG A 951 

*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 42
  time to evaluate  : 1.230 
Fit side-chains
   revert: symmetry clash
REVERT: A  321 MET cc_start: 0.8355 (mmt) cc_final: 0.8056 (mmm)
  outliers start: 4
  outliers final: 4
  residues processed: 45
  average time/residue: 0.3203
  time to fit residues: 21.0006
Evaluate side-chains
  37 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 33
  time to evaluate  : 1.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 ARG
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  305 ILE
Chi-restraints excluded: chain A residue  651 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 63 optimal weight:    2.9990
   chunk 35 optimal weight:    1.9990
   chunk 94 optimal weight:    0.6980
   chunk 77 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9990
   chunk 113 optimal weight:    2.9990
   chunk 122 optimal weight:    1.9990
   chunk 101 optimal weight:    3.9990
   chunk 112 optimal weight:    8.9990
   chunk 38 optimal weight:    0.9990
   chunk 91 optimal weight:    4.9990
   overall best weight:    1.3388

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7968
moved from start:          0.2646

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031  12742  Z= 0.278
  Angle     :  0.555   8.003  17828  Z= 0.298
  Chirality :  0.038   0.208   2061
  Planarity :  0.004   0.044   1745
  Dihedral  : 20.777 176.073   3192
  Min Nonbonded Distance : 2.335

Molprobity Statistics.
  All-atom Clashscore : 3.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.86 %
    Favored  : 95.14 %
  Rotamer:
    Outliers :  0.80 %
    Allowed  : 11.73 %
    Favored  : 87.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.95 (0.24), residues: 1110
  helix:  0.36 (0.23), residues: 536
  sheet: -1.10 (0.52), residues: 108
  loop : -1.67 (0.25), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 476 
 HIS   0.007   0.001   HIS A 167 
 PHE   0.022   0.002   PHE A 643 
 TYR   0.017   0.001   TYR A 325 
 ARG   0.004   0.001   ARG A  78 

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 36
  time to evaluate  : 1.156 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  321 MET cc_start: 0.8242 (mmt) cc_final: 0.7945 (mmm)
  outliers start: 8
  outliers final: 4
  residues processed: 42
  average time/residue: 0.2415
  time to fit residues: 16.0481
Evaluate side-chains
  36 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 32
  time to evaluate  : 1.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  651 LEU
Chi-restraints excluded: chain A residue  657 THR
Chi-restraints excluded: chain A residue 1352 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 112 optimal weight:    9.9990
   chunk 85 optimal weight:    0.8980
   chunk 59 optimal weight:    3.9990
   chunk 12 optimal weight:    0.5980
   chunk 54 optimal weight:    4.9990
   chunk 76 optimal weight:    0.9990
   chunk 114 optimal weight:    2.9990
   chunk 120 optimal weight:    4.9990
   chunk 108 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9980
   chunk 100 optimal weight:    0.0470
   overall best weight:    0.7080

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A1262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7922
moved from start:          0.2827

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  12742  Z= 0.170
  Angle     :  0.491   8.438  17828  Z= 0.263
  Chirality :  0.036   0.197   2061
  Planarity :  0.003   0.044   1745
  Dihedral  : 20.722 176.052   3192
  Min Nonbonded Distance : 2.298

Molprobity Statistics.
  All-atom Clashscore : 3.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  0.89 %
    Allowed  : 13.22 %
    Favored  : 85.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.59 (0.25), residues: 1110
  helix:  0.69 (0.23), residues: 536
  sheet: -0.83 (0.49), residues: 118
  loop : -1.56 (0.26), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 476 
 HIS   0.011   0.001   HIS A1262 
 PHE   0.009   0.001   PHE A 643 
 TYR   0.012   0.001   TYR A 325 
 ARG   0.003   0.000   ARG A 951 

*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 33
  time to evaluate  : 1.353 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 9
  outliers final: 5
  residues processed: 40
  average time/residue: 0.2405
  time to fit residues: 15.4607
Evaluate side-chains
  39 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 34
  time to evaluate  : 1.229 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  651 LEU
Chi-restraints excluded: chain A residue  657 THR
Chi-restraints excluded: chain A residue 1146 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 68 optimal weight:    0.8980
   chunk 1 optimal weight:    3.9990
   chunk 89 optimal weight:    1.9990
   chunk 49 optimal weight:    2.9990
   chunk 103 optimal weight:    1.9990
   chunk 83 optimal weight:    0.7980
   chunk 0 optimal weight:    1.9990
   chunk 61 optimal weight:    0.8980
   chunk 108 optimal weight:    1.9990
   chunk 30 optimal weight:    0.0870
   chunk 40 optimal weight:    0.5980
   overall best weight:    0.6558

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 980 ASN
A1177 ASN
** A1261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7913
moved from start:          0.2975

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  12742  Z= 0.161
  Angle     :  0.484   7.869  17828  Z= 0.257
  Chirality :  0.035   0.200   2061
  Planarity :  0.003   0.043   1745
  Dihedral  : 20.705 176.173   3192
  Min Nonbonded Distance : 2.314

Molprobity Statistics.
  All-atom Clashscore : 3.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  : 14.02 %
    Favored  : 84.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.48 (0.25), residues: 1110
  helix:  0.79 (0.23), residues: 540
  sheet: -0.76 (0.50), residues: 118
  loop : -1.53 (0.26), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 476 
 HIS   0.006   0.001   HIS A1262 
 PHE   0.009   0.001   PHE A  97 
 TYR   0.012   0.001   TYR A 325 
 ARG   0.003   0.000   ARG A 951 

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 37
  time to evaluate  : 1.326 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  534 MET cc_start: 0.0699 (ppp) cc_final: -0.0632 (ppp)
  outliers start: 14
  outliers final: 7
  residues processed: 50
  average time/residue: 0.2285
  time to fit residues: 18.4442
Evaluate side-chains
  39 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 32
  time to evaluate  : 1.191 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  651 LEU
Chi-restraints excluded: chain A residue  657 THR
Chi-restraints excluded: chain A residue 1146 VAL
Chi-restraints excluded: chain A residue 1337 THR
Chi-restraints excluded: chain A residue 1352 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 108 optimal weight:    0.9990
   chunk 23 optimal weight:    6.9990
   chunk 70 optimal weight:    3.9990
   chunk 29 optimal weight:    6.9990
   chunk 120 optimal weight:    5.9990
   chunk 100 optimal weight:    3.9990
   chunk 55 optimal weight:   10.0000
   chunk 10 optimal weight:    2.9990
   chunk 40 optimal weight:    0.0970
   chunk 63 optimal weight:    4.9990
   chunk 116 optimal weight:    3.9990
   overall best weight:    2.4186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A  46 ASN
** A1262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8044
moved from start:          0.3354

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.052  12742  Z= 0.488
  Angle     :  0.669   7.462  17828  Z= 0.353
  Chirality :  0.043   0.220   2061
  Planarity :  0.004   0.047   1745
  Dihedral  : 20.957 177.343   3192
  Min Nonbonded Distance : 2.239

Molprobity Statistics.
  All-atom Clashscore : 4.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.86 %
    Favored  : 94.14 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 15.11 %
    Favored  : 83.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.07 (0.24), residues: 1110
  helix:  0.34 (0.23), residues: 534
  sheet: -1.35 (0.51), residues: 108
  loop : -1.77 (0.25), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 476 
 HIS   0.010   0.002   HIS A 167 
 PHE   0.022   0.002   PHE A 105 
 TYR   0.021   0.002   TYR A 325 
 ARG   0.004   0.001   ARG A  78 

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 33
  time to evaluate  : 1.253 
Fit side-chains
   revert: symmetry clash
REVERT: A  321 MET cc_start: 0.8386 (mmt) cc_final: 0.8083 (mmm)
REVERT: A 1079 ASP cc_start: 0.6999 (OUTLIER) cc_final: 0.6781 (t0)
  outliers start: 18
  outliers final: 11
  residues processed: 49
  average time/residue: 0.2630
  time to fit residues: 19.9160
Evaluate side-chains
  43 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 31
  time to evaluate  : 1.373 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  305 ILE
Chi-restraints excluded: chain A residue  619 ILE
Chi-restraints excluded: chain A residue  647 VAL
Chi-restraints excluded: chain A residue  651 LEU
Chi-restraints excluded: chain A residue  657 THR
Chi-restraints excluded: chain A residue  937 SER
Chi-restraints excluded: chain A residue 1079 ASP
Chi-restraints excluded: chain A residue 1142 SER
Chi-restraints excluded: chain A residue 1146 VAL
Chi-restraints excluded: chain A residue 1352 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 13 optimal weight:    0.8980
   chunk 68 optimal weight:    3.9990
   chunk 88 optimal weight:    0.8980
   chunk 101 optimal weight:    2.9990
   chunk 67 optimal weight:    0.8980
   chunk 120 optimal weight:    4.9990
   chunk 75 optimal weight:    0.8980
   chunk 73 optimal weight:    0.5980
   chunk 55 optimal weight:   10.0000
   chunk 74 optimal weight:    0.7980
   chunk 48 optimal weight:    0.9990
   overall best weight:    0.8180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 544 GLN
A1177 ASN
** A1262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7954
moved from start:          0.3348

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  12742  Z= 0.180
  Angle     :  0.509   9.556  17828  Z= 0.270
  Chirality :  0.036   0.197   2061
  Planarity :  0.003   0.045   1745
  Dihedral  : 20.823 177.051   3192
  Min Nonbonded Distance : 2.262

Molprobity Statistics.
  All-atom Clashscore : 3.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  1.19 %
    Allowed  : 16.10 %
    Favored  : 82.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.63 (0.25), residues: 1110
  helix:  0.83 (0.23), residues: 519
  sheet: -0.97 (0.49), residues: 116
  loop : -1.69 (0.25), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 476 
 HIS   0.004   0.001   HIS A 167 
 PHE   0.010   0.001   PHE A 491 
 TYR   0.013   0.001   TYR A 325 
 ARG   0.003   0.000   ARG A  70 

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 32
  time to evaluate  : 1.246 
Fit side-chains
   revert: symmetry clash
REVERT: A  534 MET cc_start: 0.0959 (ppp) cc_final: -0.0202 (ppp)
  outliers start: 12
  outliers final: 11
  residues processed: 42
  average time/residue: 0.2368
  time to fit residues: 16.4213
Evaluate side-chains
  43 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 32
  time to evaluate  : 1.348 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  404 THR
Chi-restraints excluded: chain A residue  647 VAL
Chi-restraints excluded: chain A residue  651 LEU
Chi-restraints excluded: chain A residue  657 THR
Chi-restraints excluded: chain A residue  953 VAL
Chi-restraints excluded: chain A residue 1146 VAL
Chi-restraints excluded: chain A residue 1177 ASN
Chi-restraints excluded: chain A residue 1337 THR
Chi-restraints excluded: chain A residue 1352 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 71 optimal weight:    4.9990
   chunk 36 optimal weight:    0.9990
   chunk 23 optimal weight:    9.9990
   chunk 76 optimal weight:    0.9990
   chunk 82 optimal weight:    0.9980
   chunk 59 optimal weight:    2.9990
   chunk 11 optimal weight:    1.9990
   chunk 94 optimal weight:    1.9990
   chunk 109 optimal weight:    1.9990
   chunk 115 optimal weight:    6.9990
   chunk 105 optimal weight:    0.0170
   overall best weight:    1.0024

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A1177 ASN
** A1262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7966
moved from start:          0.3435

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  12742  Z= 0.217
  Angle     :  0.513   8.005  17828  Z= 0.274
  Chirality :  0.037   0.203   2061
  Planarity :  0.003   0.044   1745
  Dihedral  : 20.787 177.024   3192
  Min Nonbonded Distance : 2.260

Molprobity Statistics.
  All-atom Clashscore : 3.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.77 %
    Favored  : 95.23 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 15.90 %
    Favored  : 82.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.63 (0.25), residues: 1110
  helix:  0.81 (0.23), residues: 526
  sheet: -0.95 (0.50), residues: 116
  loop : -1.71 (0.25), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 476 
 HIS   0.005   0.001   HIS A 167 
 PHE   0.011   0.001   PHE A 491 
 TYR   0.014   0.001   TYR A 325 
 ARG   0.002   0.000   ARG A  70 

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 33
  time to evaluate  : 1.192 
Fit side-chains
   revert: symmetry clash
REVERT: A  534 MET cc_start: 0.1019 (ppp) cc_final: -0.0367 (ppp)
REVERT: A  648 MET cc_start: 0.6987 (mtm) cc_final: 0.6761 (mtt)
  outliers start: 15
  outliers final: 12
  residues processed: 46
  average time/residue: 0.2394
  time to fit residues: 17.6359
Evaluate side-chains
  44 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 32
  time to evaluate  : 0.812 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  184 LEU
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  404 THR
Chi-restraints excluded: chain A residue  647 VAL
Chi-restraints excluded: chain A residue  651 LEU
Chi-restraints excluded: chain A residue  657 THR
Chi-restraints excluded: chain A residue  953 VAL
Chi-restraints excluded: chain A residue 1146 VAL
Chi-restraints excluded: chain A residue 1177 ASN
Chi-restraints excluded: chain A residue 1337 THR
Chi-restraints excluded: chain A residue 1352 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 112 optimal weight:    9.9990
   chunk 115 optimal weight:    6.9990
   chunk 67 optimal weight:    2.9990
   chunk 48 optimal weight:    1.9990
   chunk 88 optimal weight:    0.9980
   chunk 34 optimal weight:    2.9990
   chunk 101 optimal weight:    4.9990
   chunk 106 optimal weight:    1.9990
   chunk 111 optimal weight:    2.9990
   chunk 73 optimal weight:    0.9990
   chunk 118 optimal weight:    3.9990
   overall best weight:    1.7988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A1262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8022
moved from start:          0.3608

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.041  12742  Z= 0.361
  Angle     :  0.603  10.093  17828  Z= 0.319
  Chirality :  0.040   0.210   2061
  Planarity :  0.004   0.047   1745
  Dihedral  : 20.870 177.348   3192
  Min Nonbonded Distance : 2.234

Molprobity Statistics.
  All-atom Clashscore : 3.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.14 %
    Favored  : 94.86 %
  Rotamer:
    Outliers :  1.19 %
    Allowed  : 16.30 %
    Favored  : 82.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.90 (0.24), residues: 1110
  helix:  0.52 (0.23), residues: 530
  sheet: -1.08 (0.50), residues: 116
  loop : -1.77 (0.25), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 476 
 HIS   0.008   0.001   HIS A 167 
 PHE   0.016   0.002   PHE A 105 
 TYR   0.018   0.002   TYR A 325 
 ARG   0.004   0.000   ARG A  78 

*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 31
  time to evaluate  : 1.166 
Fit side-chains
   revert: symmetry clash
REVERT: A  534 MET cc_start: 0.1176 (ppp) cc_final: -0.0310 (ppp)
  outliers start: 12
  outliers final: 12
  residues processed: 42
  average time/residue: 0.2333
  time to fit residues: 16.0369
Evaluate side-chains
  42 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 30
  time to evaluate  : 1.174 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  123 VAL
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  184 LEU
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  339 VAL
Chi-restraints excluded: chain A residue  404 THR
Chi-restraints excluded: chain A residue  647 VAL
Chi-restraints excluded: chain A residue  651 LEU
Chi-restraints excluded: chain A residue  657 THR
Chi-restraints excluded: chain A residue  953 VAL
Chi-restraints excluded: chain A residue 1146 VAL
Chi-restraints excluded: chain A residue 1352 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 72 optimal weight:    0.6980
   chunk 56 optimal weight:    2.9990
   chunk 82 optimal weight:    1.9990
   chunk 124 optimal weight:    3.9990
   chunk 114 optimal weight:    2.9990
   chunk 99 optimal weight:    2.9990
   chunk 10 optimal weight:    0.6980
   chunk 76 optimal weight:    0.9980
   chunk 60 optimal weight:    3.9990
   chunk 78 optimal weight:    0.9990
   chunk 105 optimal weight:    1.9990
   overall best weight:    1.0784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A1262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7980
moved from start:          0.3628
Sorry: Reduce crashed with command 'molprobity.reduce  -quiet -trim -'.
Dumping stdin to file 'reduce_fail.pdb'.
Return code: -15
Dumping stderr: